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Dr. Martin Harris (Liam Neeson) and his wife Liz (January Jones) arrive in Berlin for a biotechnology summit. Upon arriving at their hotel, Martin realizes he forgot his briefcase at the airport. He takes a taxicab driven by Gina (Diane Kruger), but on the way to the airport, the cab crashes off a bridge into the river after narrowly avoiding a refrigerator that falls off a delivery truck. Martin is knocked unconscious upon impact, but Gina saves him from drowning before fleeing from the scene to avoid the police, since she is an illegal immigrant from Bosnia. On Thanksgiving day, he gains consciousness at the hospital after being in a coma for four days.

Martin returns to his hotel, only to discover another man (Aidan Quinn) with his wife, who tells hotel security she does not know him. He attempts to contact his old colleague Prof. Rodney Cole (Frank Langella), who is unavailable due to Thanksgiving in the United States. Martin then heads to the office of Prof. Bressler, whom he is scheduled to meet that day. However, he sees the impostor, "Martin B" already in a meeting with Bressler. As Martin attempts to prove his identity, Martin B shows him his ID and family photo – both of which have Martin's name, only with his face replaced by that of the impostor. Disillusioned by the identity crisis, Martin falls unconscious and finds himself back at the hospital, where he undergoes an MRI to see if the accident had caused any head trauma. An assassin sent to target him kills Nurse Gretchen Erfurt, but Martin escapes.

He then seeks help from Nurse Erfurt's friend, private investigator and former Stasi agent Ernst Jürgen (Bruno Ganz). Martin's only clues are his notebook and Gina, who works at a diner after being fired from the taxicab company since the incident. While Martin attempts to persuade Gina into helping him clear up his identity problem, Jürgen digs up information related to Martin and the biotechnology summit. He discovers that the summit is to be attended by Prince Shada of Saudi Arabia, who is funding a secret project headed by Bressler. Prince Shada has survived numerous assassination attempts from extremists in his own country, and Jürgen suspects that Martin's identity theft may be another attempt at taking the Prince's life. Jürgen receives Cole at his office, but since he realizes that Cole is not who he says he is (surmising that Cole is a member of a secret assassination unit), he commits suicide by drinking cyanide-laced coffee. He also has figured out who Martin really is (also a member of the same unit), because his last words are to ask Cole, "What if he [meaning Harris] remembers everything?"

Meanwhile, the assassins attempt to eliminate Martin and Gina, but the couple escape after a fight at her apartment and a lengthy car chase. Martin looks at his notebook and sees a set of numbers written by his wife. The numbers correspond to words found on specific pages of the notebook, which appear as secret codes. Using the schedule written on the notebook, Martin confronts Liz, who tells him that he left his briefcase at the airport. After retrieving it, Martin parts ways with Gina. She sees him kidnapped by Cole and his henchman Jones. Gina steals a taxicab and chases after Cole's van. Martin wakes up in a car park and discovers the truth of his identity from Cole. It is revealed that Martin Harris is a cover name, and that he, Liz and Martin B are assassins sent to target the summit. Because he injured his head during the car crash, his memory was altered and he believed that Martin Harris was his real life identity. However, he still does not remember his own true identity. Gina rushes in and stops Jones from killing Martin as Cole hides in his van. There is a brief fight between Jones and Gina that ends when Gina drives her car into Jones and squashes him against Cole's van. The impact of the crash also sends the van plummeting out the car park with Cole still inside. Martin discovers a hidden compartment in his briefcase and finds two Canadian passports, realizing he and Liz were in Berlin three months prior to plant a bomb in the suite that is to be occupied later by them for the summit.

The duo head for the hotel to stop the assassination. They are immediately arrested by security, but Martin convinces them of his presence in the hotel three months back. He then realizes that Prince Shada is not the target, but Bressler – who has discovered a genetically modified breed of corn that is capable of surviving any climate, easing the world's food supply problem. Liz uses her own copy of the notebook's secret codes to remotely access Bressler's laptop and steal the data. After being convinced there is a bomb, security evacuates the hotel. Seeing that their assassination attempt has been foiled, Liz tries to disarm the bomb, but is too late and is killed as a section of the hotel is blown up. Martin B, the last remaining assassin, attempts to kill Prof. Bressler, but Martin fights and kills him. Bressler later announces his project to the world, and Martin and Gina board a train with passports, which give them new identities